calcNormFactors(edgeR)
calcNormFactors()所属R语言包：edgeR
Calculates Normalization Factors for a Matrix of Count Data
计算矩阵的计数数据的规范化因素
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Using a reference sample, calculate the normalization factors, over and above accounting for library size.
使用一个参考样本，计算标准化的因素，远远超过占库的大小。
用法----------Usage----------
calcNormFactors(object, method=c("TMM","RLE","upperquartile"), refColumn = NULL, logratioTrim = .3, sumTrim = 0.05, doWeighting=TRUE, Acutoff=-1e10, p=0.75)
参数----------Arguments----------
参数：object
either a matrix of raw (read) counts or a DGEList object
无论是原料（只读）计数matrix或DGEList对象
参数：method
method to use to calculate the scale factors
使用的方法计算规模因素
参数：refColumn
column to use as reference, only used when method="TMM"
列作为参考使用，仅用于method="TMM"
参数：logratioTrim
amount of trim to use on log-ratios ("M" values), only used when method="TMM"
适量修剪使用log比率（“M”的值），只用时method="TMM"
参数：sumTrim
amount of trim to use on the combined absolute levels ("A" values), only used when method="TMM"
修剪量使用上的合并（“A”的值）的绝对水平，只用时method="TMM"
参数：doWeighting
logical, whether to compute (asymptotic binomial precision) weights, only used when method="TMM"
逻辑，是否计算（渐近二项式精度）的重量，只用时method="TMM"
参数：Acutoff
cutoff on "A" values to use before trimming, only used when method="TMM"
截止上“A”的值，使用前修剪，只用时method="TMM"
参数：p
percentile (between 0 and 1) used to compute scale factors from, only used when method="upperquartile"
百分（0和1之间），用于计算规模因素，只用时method="upperquartile"
Details
详情----------Details----------
method="TMM" is the weighted trimmed mean of M-values (to the reference) proposed by Robinson and Oshlack (2010), where the weights are from the delta method on Binomial data. If refColumn is unspecified, the library whose upper quartile is closest to the mean upper quartile is used.
method="TMM"是修剪加权平均的M值（参考）提出罗宾逊和Oshlack的（2010），其中重增量从二项式数据的方法。 refColumn如果是不确定的，用于库的上四分位值是最接近平均的上四分。
method="RLE" is the scaling factor method proposed by Anders and Huber (2010). We call it "relative log expression", as median library is calculated from the geometric mean of all columns and the median ratio of each sample to the median library is taken as the scale factor.
method="RLE"是安德斯和Huber（2010）所提出的比例因子的方法。我们称之为“相对表达log”，以中位数库的所有列和每个样本的中位数比中位数库的几何平均数计算规模因素。
method="upperquartile" is the upper-quartile normalization method of Bullard et al (2010), in which the scale factors are calculated from the 75% quantile of the counts for each library, after removing transcripts which are zero in all libraries. We generalize it to allow scaling by any quantile of the distributions.
method="upperquartile"是上四分标准化布拉德等人（2010），其中规模因素的消除零，这是在所有图书馆的成绩单后，为每个库数的75％分位数计算方法。我们概括它允许任何尺度分布的分位数。
For symmetry, normalization factors are adjusted to multiply to 1.
为对称性，标准化的因素调整乘以1。
值----------Value----------
If a matrix is given for object, the output is a vector with length ncol(object) giving the relative normalization factors. If a DGEList object is given for object, the output is a DGEList object containing the normalization factors in the samples$norm.factors element.
如果matrixobject，输出的是一个向量长度ncol(object)给相对标准化因素。 DGEList如果object对象，输出是一个DGEList对象包含在samples$norm.factors元素标准化的因素。
作者（S）----------Author(s)----------
Mark Robinson
参考文献----------References----------
Differential expression analysis for sequence count data Genome Biology 11, R106.
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11, 94. A scaling normalization method for differential expression analysis of RNA-seq data.
Genome Biology 11, R25.
举例----------Examples----------
d <- matrix( rpois(1000, lambda=5), nrow=200 )
f <- calcNormFactors(d)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-2-25 17:03:44
